Nonprotein-Coding RNAs as Regulators of Development in Tunicates
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Tunicates, or urochordates, are a group of small marine organisms that are found widely throughout the seas of the world. As most plausible sister group of the vertebrates, they are of utmost importance for a comprehensive understanding of chordate evolution; hence, they have served as model organisms for many aspects of the developmental biology. Current genomic analysis of tunicates indicates that their genomes evolved with a fast rate not only at the level of nucleotide substitutions but also in terms of genomic organization. The latter involves genome reduction, rearrangements, as well as the loss of some important coding and noncoding RNA (ncRNAs) elements and even entire genomic regions that are otherwise well conserved. These observations are largely based on evidence from comparative genomics resulting from the analysis of well-studied gene families such as the Hox genes and their noncoding elements. In this chapter, the focus lies on the ncRNA complement of tunicates, with a particular emphasis on microRNAs, which have already been studied extensively for other animal clades. MicroRNAs are known as important regulators of key genes in animal development, and they are intimately related to the increase morphological complexity in higher metazoans. Here we review the discovery, evolution, and genome organization of the miRNA repertoire, which has been drastically reduced and restructured in tunicates compared to the chordate ancestor. Known functions of microRNAs as regulators of development in tunicates are a central topic. For instance, we consider the role of miRNAs as regulators of the muscle development and their importance in the regulation of the differential expression during the oral siphon regeneration. Beyond microRNAs, we touch upon the functions of some other ncRNAs such as yellow crescent RNA, moRNAs, RMST lncRNAs, or spliced-leader (SL) RNAs, which have diverse functions associated with the embryonic development, neurogenesis, and mediation of mRNA stability in general.
This work and the computational analysis were partially supported by the equipment donation from the German Academic Exchange Service—DAAD to the Faculty of Science at the Universidad Nacional de Colombia and by the computational laboratory from Bioinformatics Group at the Department of Computer Science and Interdisciplinary Center for Bioinformatics at the Leipzig University. The comparative analysis was partially supported by Colciencias (project no. 110165843196, contract 571-2014). CAVH acknowledges the support by DAAD scholarship: Forschungsstipendien-Promotionen in Deutschland, 2017/2018 (Bewerbung 57299294). CIBS acknowledges Universidad Nacional de Colombia for the time granted to write this chapter. FDB was supported by a FAPESP JP 2015/50164-5 (ANR collaborative grant).
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